[English] 日本語
Yorodumi
- PDB-1qfh: DIMERIZATION OF GELATION FACTOR FROM DICTYOSTELIUM DISCOIDEUM: CR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qfh
TitleDIMERIZATION OF GELATION FACTOR FROM DICTYOSTELIUM DISCOIDEUM: CRYSTAL STRUCTURE OF ROD DOMAINS 5 AND 6
ComponentsPROTEIN (GELATION FACTOR)
KeywordsACTIN BINDING PROTEIN / IMMUNOGLOBULIN / GELATION FACTOR / ABP-120
Function / homology
Function and homology information


regulation of pseudopodium assembly / anterior cell cortex / Cell-extracellular matrix interactions / pseudopodium assembly / ISG15 antiviral mechanism / Platelet degranulation / sorocarp development / posterior cell cortex / chemotaxis to cAMP / lateral cell cortex ...regulation of pseudopodium assembly / anterior cell cortex / Cell-extracellular matrix interactions / pseudopodium assembly / ISG15 antiviral mechanism / Platelet degranulation / sorocarp development / posterior cell cortex / chemotaxis to cAMP / lateral cell cortex / phototaxis / macropinocytic cup / RHO GTPases activate PAKs / protein kinase B binding / actin crosslink formation / thermotaxis / hyperosmotic response / mitogen-activated protein kinase binding / lamellipodium assembly / cortical actin cytoskeleton / cell leading edge / pseudopodium / phagocytic cup / phagocytosis / response to cAMP / extracellular matrix / cell motility / small GTPase binding / actin filament binding / cell migration / cell cortex / actin cytoskeleton organization / plasma membrane / cytoplasm
Similarity search - Function
Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain ...Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsMccoy, A.J. / Fucini, P. / Noegel, A.A. / Stewart, M.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: Structural basis for dimerization of the Dictyostelium gelation factor (ABP120) rod.
Authors: McCoy, A.J. / Fucini, P. / Noegel, A.A. / Stewart, M.
#1: Journal: J.Struct.Biol. / Year: 1997
Title: Crystallization and preliminary X-Ray diffraction characterization of a dimerizing fragment of the rod domain of the Dictyostelium gelation factor (ABP-120).
Authors: Fucini, P. / McCoy, A.J. / Gomez-Ortiz, M. / Schleicher, M. / Noegel, A.A. / Stewart, M.
History
DepositionApr 11, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 27, 2019Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (GELATION FACTOR)
B: PROTEIN (GELATION FACTOR)


Theoretical massNumber of molelcules
Total (without water)44,7112
Polymers44,7112
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-13 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.448, 103.150, 124.361
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.64641, -0.680864, 0.344352), (-0.663308, -0.724509, -0.187375), (0.377063, -0.107291, -0.919952)12.968, 33.09, 2.675
2given(0.606333, -0.678262, 0.415115), (-0.700719, -0.702516, -0.124355), (0.375971, -0.215478, -0.90123)14.929, 33.123, 0.304

-
Components

#1: Protein PROTEIN (GELATION FACTOR) / ACTIN BINDING PROTEIN 120 / Dictyostelium filamin / ddFLN


Mass: 22355.594 Da / Num. of mol.: 2 / Fragment: ROD DOMAINS 5 AMD 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: P13466
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.2 / Details: 30% PEG 1000, 0.1M TRIS_HCL PH 7.2, 25% GLYCEROL
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.6 mg/mlprotein11
220 mMpotassium phosphate12
3100 mM12NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.88
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 2.2→26.23 Å / Num. obs: 82513 / % possible obs: 98 % / Redundancy: 2.9 % / Biso Wilson estimate: 29.87 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 8.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.091 / Mean I/σ(I) obs: 6.9 / % possible all: 97.6
Reflection
*PLUS
Num. obs: 28551 / % possible obs: 98 % / Num. measured all: 82513
Reflection shell
*PLUS
% possible obs: 97.6 % / Num. unique obs: 4076 / Num. measured obs: 11993

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→26.63 Å / SU B: 5.42051 / SU ML: 0.14239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24148 / ESU R Free: 0.20983
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1442 5 %RANDOM
Rwork0.2216 ---
obs0.2192 28503 98 %-
Displacement parametersBiso mean: 42.59 Å2
Refinement stepCycle: LAST / Resolution: 2.2→26.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3100 0 0 237 3337
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.018
X-RAY DIFFRACTIONp_angle_d0.0190.019
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.713
X-RAY DIFFRACTIONp_mcangle_it2.4945
X-RAY DIFFRACTIONp_scbond_it3.0354
X-RAY DIFFRACTIONp_scangle_it4.3126
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1280.15
X-RAY DIFFRACTIONp_singtor_nbd00.05
X-RAY DIFFRACTIONp_multtor_nbd00.05
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.0610.05
X-RAY DIFFRACTIONp_planar_tor3.77
X-RAY DIFFRACTIONp_staggered_tor13.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor1420
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more